This set of Bioinformatics Multiple Choice Questions & Answers (MCQs) focuses on “Phylogenetic Programs”.
1. PAUP is a Macintosh program (UNIX version available in the GCG package) with a very user-friendly graphical interface.
a) True
b) False
View Answer
Explanation: It stands for Phylogenetic analysis using parsimony. It is a commercial phylogenetic package. It is probably one of the most widely used phylogenetic programs available from Sinauer Publishers. PAUP was originally developed as parsimony program, but expanded to a comprehensive package that is capable of performing distance, parsimony, and likelihood analyses.
2. In PAUP, The distance options include NJ, ME, FM, and UPGMA.
a) True
b) False
View Answer
Explanation: For distance or ML analyses, PAUP has the option for detailed specifications of substitution models, base frequencies, and among site rate heterogeneity (γ -shape parameters, proportion of invariant sites). PAUP is also able to perform nonparametric bootstrapping, jackknifing, KH testing, and SH testing.
3. Phylip stands for Phylogenetic inference package (by Joe Felsenstein).
a) True
b) False
View Answer
Explanation: Is a free multiplatform comprehensive package containing thirty-five subprograms for performing distance, parsimony, and likelihood analysis, as well as bootstrapping for both nucleotide and amino acid sequences.
4. In PAUP, to complete an analysis the user is not required to move between different subprograms while keeping modifying names of the intermediate output files.
a) True
b) False
View Answer
Explanation: The only problem is that to complete an analysis the user is required to move between different subprograms while keeping modifying names of the intermediate output files. It is command-line based, but relatively easy to use for each single program.
5. Which of the following is untrue regarding TREE-PUZZLE?
a) It is a program performing quartet puzzling
b) It allows various substitution models for likelihood score estimation
c) It doesn’t incorporate a discrete γ model
d) Because of the heuristic nature of the program, it allows ML analyses of large datasets
View Answer
Explanation: The advantage is that it allows various substitution models for likelihood score estimation. Also, it incorporates a discrete γ model for rate heterogeneity among sites.
6. Which of the following is untrue regarding TREE-PUZZLE?
a) The resulting puzzle trees are automatically assigned puzzle support values to internal branches
b) The support values are percentages of consistent quartet trees
c) The support values do not have the same meaning as bootstrap values
d) The support values have the same meaning as bootstrap values
View Answer
Explanation: Because of the heuristic nature of the program, it allows ML analyses of large datasets. TREE-PUZZLE version 5.0 is available for Mac, UNIX, and Windows.
7. PHYML is a web-based _______ program using the _____
a) phylogenetic, GA (Genetic Algorithm)
b) sequence based alignment, GA (Genetic Algorithm)
c) phylogenetic, dynamic programming
d) sequence based alignment, dynamic programming
View Answer
Explanation: It first builds an NJ tree. Further it uses it as a starting tree for subsequent iterative refinement through subtree swapping. Branch lengths are simultaneously optimized during this process.
8. In PHYML, The tree searching _____ when the total ML score no longer ______
a) ceases, increases
b) stops, decreases
c) terminates, decreases
d) stops, increases
View Answer
Explanation: PHYML is a web-based phylogenetic program using the GA. The main advantage of this program is the ability to build trees from very large datasets with hundreds of taxa and to complete tree searching within a relatively short time frame.
9. MrBayes is a Bayesian phylogenetic inference program.
a) True
b) False
View Answer
Explanation: It randomly samples tree topologies using the MCMC procedure. Next it infers the posterior distribution of tree topologies.
10. MrBayes has a range of probabilistic models available to search for a set of trees with the lowest posterior probability.
a) True
b) False
View Answer
Explanation: MrBayes has a range of probabilistic models available to search for a set of trees with the highest posterior probability. It is fast and capable of handling large datasets. The program is available in multi platform versions. A web program that also employs Bayesian inference for phylogenetic analysis is BAMBE.
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